If you're not guiding with an OAG, then the guide camera isn't being rotated when the rotator for the imaging camera is moved. So your PHD2 configuration profile should not include a connection to the rotator.
We have tried to make this clear in both the User Guide and the new-profile-wizard but maybe we have come up short:
User Guide:
PHD2 does not control a rotator, but
it will read the current angle setting from the rotator and adjust
the guiding calibration if needed. Rotators are used to control
the orientation of the imaging camera with respect to the sky - perhaps
to keep the orientation the same on opposite sides of the pier or to
create a favorable composition of the objects in the field of view.
If the rotator is part of an off-axis-guider assembly, its
rotation will affect the PHD2 calibration. In this situation,
PHD2 should be connected to the rotator so the calibration can be
adjusted automatically.
New-profile-wizard:
So, perhaps we should extend the sentence in the User Guide to say "otherwise, you should not connect PHD2 to the rotator".
The point of all this is that PHD2 has to know the angular orientation of the guide camera relative to the sky - that's the only way it can translate the X/Y movements of the guide star on the camera sensor into the RA/Dec movements of the mount axes. It's essentially a transformation from the X/Y coordinate system of the camera sensor into the RA/Dec coordinate system of the mount and the nighttime sky.
With regard to the RA tracking errors you are looking at, the session beginning at 22:43 shows some fairly nasty problems. Here is a look at the unguided RA tracking during that period.
If you look at the errors identified by the red arrows, you can see there are some rather abrupt large errors - errors of many arc-sec that occur during intervals of a minute or less. This is not typical periodic error which usually produces a relatively smooth sine-wave pattern. Abrupt errors like this are going to be hard to guide out. It would be good if you could get some help from the manufacturer of your mount to see if you can get improvements via mechanical adjustment. Sometimes, these kinds of problems can be caused by a drive system that is too tightly meshed.
Regards,
Bruce